ergo
xyz_file_parser.h
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1 /* Ergo, version 3.8, a program for linear scaling electronic structure
2  * calculations.
3  * Copyright (C) 2019 Elias Rudberg, Emanuel H. Rubensson, Pawel Salek,
4  * and Anastasia Kruchinina.
5  *
6  * This program is free software: you can redistribute it and/or modify
7  * it under the terms of the GNU General Public License as published by
8  * the Free Software Foundation, either version 3 of the License, or
9  * (at your option) any later version.
10  *
11  * This program is distributed in the hope that it will be useful,
12  * but WITHOUT ANY WARRANTY; without even the implied warranty of
13  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
14  * GNU General Public License for more details.
15  *
16  * You should have received a copy of the GNU General Public License
17  * along with this program. If not, see <http://www.gnu.org/licenses/>.
18  *
19  * Primary academic reference:
20  * Ergo: An open-source program for linear-scaling electronic structure
21  * calculations,
22  * Elias Rudberg, Emanuel H. Rubensson, Pawel Salek, and Anastasia
23  * Kruchinina,
24  * SoftwareX 7, 107 (2018),
25  * <http://dx.doi.org/10.1016/j.softx.2018.03.005>
26  *
27  * For further information about Ergo, see <http://www.ergoscf.org>.
28  */
29 
38 #ifndef XYZ_FILE_PARSER_HEADER
39 #define XYZ_FILE_PARSER_HEADER
40 
41 #include "realtype.h"
42 #include "molecule.h"
43 
45  const char* fileName,
46  int netCharge,
47  bool expectPlainCharges);
48 
49 
50 #endif
realtype.h
Definition of the main floating-point datatype used; the ergo_real type.
xyz_file_parser.h
Functionality for parsing a file in xyz file format, storing the result as a molecule object.
readMoleculeFileInXyzFormat
int readMoleculeFileInXyzFormat(Molecule &result, const char *fileName, int netCharge, bool expectPlainCharges)
Definition: xyz_file_parser.cc:53
memorymanag.h
Memory allocation/deallocation routines.
UNIT_one_Angstrom
#define UNIT_one_Angstrom
Definition: units.h:43
LOG_CAT_ERROR
#define LOG_CAT_ERROR
Definition: output.h:47
atom_labels.h
Provides a way to map atom labels to their charges. The main procedure provided by this file is get_c...
ergo_real
double ergo_real
Definition: realtype.h:69
Molecule::getNoOfAtoms
int getNoOfAtoms() const
Definition: molecule.h:114
get_charge_int_from_atom_label
int get_charge_int_from_atom_label(const char *atomLabel)
Definition: atom_labels.cc:111
Molecule::setNetCharge
void setNetCharge(ergo_real netCharge_)
Definition: molecule.h:109
mat::get_file_size
static long int get_file_size(const char *fileName)
Definition: FileWritable.cc:402
utilities.h
Basic OS access utilities.
LOG_CAT_INFO
#define LOG_CAT_INFO
Definition: output.h:49
LOG_AREA_MAIN
#define LOG_AREA_MAIN
Definition: output.h:57
units.h
Constants for conversion between units for some common units like Angstrom, electron-volt (eV),...
molecule.h
Class representing a molecule as a set of atoms with assiciated coordinates and charges of the atomic...
Molecule
Representation of a molecule as a set of nuclei and total charge.
Definition: molecule.h:87
Molecule::addAtom
void addAtom(ergo_real c, ergo_real x, ergo_real y, ergo_real z)
Definition: molecule.h:97
do_output
void do_output(int logCategory, int logArea, const char *format,...)
Definition: output.cc:53
readMoleculeFileInXyzFormat
int readMoleculeFileInXyzFormat(Molecule &result, const char *fileName, int netCharge, bool expectPlainCharges)
Definition: xyz_file_parser.cc:53
output.h
Functionality for writing output messages to a text file.